1O9H | pdb_00001o9h

rRNA methyltransferase aviRa from Streptomyces viridochromogenes at 2.4A

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O9G	PDB ENTRY 1O9G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.6		MES 6.6,PEG 20K 11%, pH 6.60

Crystal Properties
Matthews coefficient	Solvent content
2.14	39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.098	α = 90
b = 48.937	β = 99.05
c = 63.714	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	287	AREA DETECTOR	BRUKER		2002-01-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.4	26.4	90	0.071	38.7	2.3		8039		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.46	90		0.282	3.2	1.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1O9G	2.4	26.44	7709	382	90.1	0.211	0.209	0.21	0.241	0.24	RANDOM	49.48

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-2.64		-0.55	2.77		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	4.981
r_scangle_it	3.112
r_mcangle_it	1.703
r_scbond_it	1.66
r_angle_refined_deg	1.188
r_mcbond_it	0.912
r_angle_other_deg	0.779
r_nbd_other	0.218
r_symmetry_vdw_other	0.214
r_nbd_refined	0.196
r_xyhbond_nbd_refined	0.175
r_symmetry_vdw_refined	0.144
r_nbtor_other	0.083
r_symmetry_hbond_refined	0.065
r_chiral_restr	0.061
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1868
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing